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  <div class="section" id="input-script-parameters">
<h1>Input script parameters<a class="headerlink" href="#input-script-parameters" title="Permalink to this headline">¶</a></h1>
<p>This is a list of the input parameter names recognized by
calc_stacking_fault_map_2D.py.</p>
<div class="section" id="global-metadata-parameters">
<h2>Global metadata parameters<a class="headerlink" href="#global-metadata-parameters" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p><strong>branch</strong>: assigns a group/branch descriptor to the calculation
which can help with parsing results later. Default value is ‘main’.</p></li>
</ul>
</div>
<div class="section" id="command-lines-for-lammps-and-mpi">
<h2>Command lines for LAMMPS and MPI<a class="headerlink" href="#command-lines-for-lammps-and-mpi" title="Permalink to this headline">¶</a></h2>
<p>Provides the external commands for running LAMMPS and MPI.</p>
<ul class="simple">
<li><p><strong>lammps_command</strong>: the path to the executable for running LAMMPS on
your system. Don’t include command line options.</p></li>
<li><p><strong>mpi_command</strong>: the path to the MPI executable and any command line
options to use for calling LAMMPS to run in parallel on your system.
Default value is None (run LAMMPS as a serial process).</p></li>
</ul>
</div>
<div class="section" id="potential-definition-and-directory-containing-associated-files">
<h2>Potential definition and directory containing associated files<a class="headerlink" href="#potential-definition-and-directory-containing-associated-files" title="Permalink to this headline">¶</a></h2>
<p>Provides the information associated with an interatomic potential
implemented for LAMMPS.</p>
<ul class="simple">
<li><p><strong>potential_file</strong>: the path to the potential_LAMMPS data model used
by atomman to generate the proper LAMMPS commands for an interatomic
potential.</p></li>
<li><p><strong>potential_dir</strong>: the path to the directory containing any potential
artifacts (eg. eam.alloy setfl files) that are used. If not given,
then any required files are expected to be in the working directory
where the calculation is executed.</p></li>
</ul>
</div>
<div class="section" id="initial-system-configuration-to-load">
<h2>Initial system configuration to load<a class="headerlink" href="#initial-system-configuration-to-load" title="Permalink to this headline">¶</a></h2>
<p>Provides the information associated with loading an atomic
configuration.</p>
<ul class="simple">
<li><p><strong>load_file</strong>: the path to the initial configuration file being read
in.</p></li>
<li><p><strong>load_style</strong>: the style/format for the load_file. The style can be
any file type supported by atomman.load()</p></li>
<li><p><strong>load_options</strong>: a list of key-value pairs for the optional
style-dependent arguments used by atomman.load().</p></li>
<li><p><strong>family</strong>: specifies the configuration family to associate with the
loaded file. This is typically a crystal structure/prototype
identifier that helps with linking calculations on the same material
together. If not given and the load_style is system_model, then the
family will be taken from the file if included. Otherwise, the family
will be taken as load_file stripped of path and extension.</p></li>
<li><p><strong>symbols</strong>: a space-delimited list of the potential’s atom-model
symbols to associate with the loaded system’s atom types. Required if
load_file does not contain this information.</p></li>
<li><p><strong>box_parameters</strong>: <em>Note that this parameter has no influence on
this calculation.</em> allows for the specification of new box parameters
to scale the loaded configuration by. This is useful for running
calculations based on prototype configurations that do not contain
material-specific dimensions. Can be given either as a list of three
or six numbers, with an optional unit of length at the end. If the
unit of length is not given, the specified length_unit (below) will
be used.</p>
<ul>
<li><p>a b c (unit): for orthogonal boxes.</p></li>
<li><p>a b c alpha beta gamma (unit): for triclinic boxes. The angles are
taken in degrees.</p></li>
</ul>
</li>
</ul>
</div>
<div class="section" id="stacking-fault-defect-parameters">
<h2>Stacking Fault Defect Parameters<a class="headerlink" href="#stacking-fault-defect-parameters" title="Permalink to this headline">¶</a></h2>
<p>Defines a stacking fault defect system to construct and analyze.</p>
<ul class="simple">
<li><p><strong>stackingfault_file</strong>: the path to a stacking-fault record file that
contains a set of input parameters associated with a specific
generalized stacking fault plane.</p></li>
<li><p><strong>stackingfault_hkl</strong> three integers for the Miller (hkl) or
Miller-Bravais (hkil) plane to create the free surface on.</p></li>
<li><p><strong>stackingfault_a1vect_uvw, stackingfault_a2vect_uvw</strong>: three
floating point numbers each that define the two directions of
shifting associated with the 2D generalized stacking fault. This is
taken as a crystallographic vector relative to the box vectors of the
initial load configuration file. This is done so that these values
have crystallographic meaning instead of just numerical meaning. Both
vectors should be within the fault plane. Ideally, they should be set
such that applying a full shiftvector shifts the system from one
perfect periodic configuration to the next.</p></li>
<li><p><strong>stackingfault_cellsetting</strong> indicates the conventional cell setting
for the crystal to use for specifying <em>surface_hkl</em> if the given unit
cell is primitive. Values are ‘p’, ‘c’, ‘i’, ‘a’, ‘b’ and ‘c’.
Default value is ‘p’, i.e. the hkl values will be taken as directly
related to the loaded unit cell.</p></li>
<li><p><strong>stackingfault_cutboxvector</strong> specifies which of the three box
vectors (‘a’, ‘b’, or ‘c’) is to be made non-periodic to create the
free surface. Default value is ‘c’.</p></li>
<li><p><strong>stackingfault_shiftindex</strong>: integer indicating which rigid body
shift to apply to the system before making the cut. This effectively
controls the atomic termination planes.</p></li>
<li><p><strong>stackingfault_faultpos</strong>: specifies a fractional coordinate from 0
to 1 indicating where along the planeaxis direction in the crystal to
position the fault plane. Default value is 0.5, which if
stackingfault_even is True will result in the same termination planes
at the free surface and the stacking fault.</p></li>
<li><p><strong>sizemults</strong>: three integers specifying the box size multiplications
to use.</p></li>
<li><p><strong>stackingfault_minwidth</strong>: floating point number stating the minimum
width along the cutboxvector direction that the system must be. The
associated sizemult value will be increased if necessary. Default
value is 0.0.</p></li>
<li><p><strong>stackingfault_even</strong>: boolean indicating if the number of replicas
in the cutboxvector direction must be even. Default value is False.</p></li>
</ul>
</div>
<div class="section" id="units-for-input-output-values">
<h2>Units for input/output values<a class="headerlink" href="#units-for-input-output-values" title="Permalink to this headline">¶</a></h2>
<p>Specifies the units for various physical quantities to use when saving
values to the results record file. Also used as the default units for
parameters in this input parameter file.</p>
<ul class="simple">
<li><p><strong>length_unit</strong>: defines the unit of length for results, and input
parameters if not directly specified. Default value is ‘angstrom’.</p></li>
<li><p><strong>energy_unit</strong>: defines the unit of energy for results, and input
parameters if not directly specified. Default value is ‘eV’.</p></li>
<li><p><strong>pressure_unit</strong>: defines the unit of pressure for results, and
input parameters if not directly specified. Default value is ‘GPa’.</p></li>
<li><p><strong>force_unit</strong>: defines the unit of pressure for results, and input
parameters if not directly specified. Default value is ‘eV/angstrom’.</p></li>
</ul>
</div>
<div class="section" id="lammps-minimization-parameters">
<h2>LAMMPS minimization parameters<a class="headerlink" href="#lammps-minimization-parameters" title="Permalink to this headline">¶</a></h2>
<p>Specifies the run parameters associated with an energy/force
minimization in LAMMPS.</p>
<ul class="simple">
<li><p><strong>energytolerance</strong>: specifies the energy tolerance to use for the
minimization. This value is unitless and corresponds to the etol term
for the <a class="reference external" href="http://lammps.sandia.gov/doc/minimize.html">LAMMPS minimize
command.</a> Default
value is 0.</p></li>
<li><p><strong>forcetolerance</strong>: specifies the force tolerance to use for the
minimization. This value is in force units and corresponds to the
ftol term for the <a class="reference external" href="http://lammps.sandia.gov/doc/minimize.html">LAMMPS minimize
command.</a> Default
value is ‘1.0e-10 eV/angstrom’.</p></li>
<li><p><strong>maxiterations</strong>: specifies the maximum number of iterations to use
for the minimization. This value corresponds to the maxiter term for
the <a class="reference external" href="http://lammps.sandia.gov/doc/minimize.html">LAMMPS minimize
command.</a> Default
value is 1000.</p></li>
<li><p><strong>maxevaluations</strong>: specifies the maximum number of iterations to use
for the minimization. This value corresponds to the maxeval term for
the <a class="reference external" href="http://lammps.sandia.gov/doc/minimize.html">LAMMPS minimize
command.</a> Default
value is 10000.</p></li>
<li><p><strong>maxatommotion</strong>: specifies the maximum distance that any atom can
move during a minimization iteration. This value is in units length
and corresponds to the dmax term for the <a class="reference external" href="http://lammps.sandia.gov/doc/min_modify.html">LAMMPS min_modify
command.</a> Default
value is ‘0.01 angstrom’.</p></li>
</ul>
</div>
<div class="section" id="run-parameters">
<h2>Run parameters<a class="headerlink" href="#run-parameters" title="Permalink to this headline">¶</a></h2>
<p>Provides parameters specific to the calculation at hand.</p>
<ul class="simple">
<li><p><strong>stackingfault_num_a1, stackingfault_num_a2</strong>: specifies the number
of shift steps to divide the shift vector directions up into. Default
value is 10 for both.</p></li>
</ul>
</div>
</div>


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  <h3><a href="../../index.html">Table of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">Input script parameters</a><ul>
<li><a class="reference internal" href="#global-metadata-parameters">Global metadata parameters</a></li>
<li><a class="reference internal" href="#command-lines-for-lammps-and-mpi">Command lines for LAMMPS and MPI</a></li>
<li><a class="reference internal" href="#potential-definition-and-directory-containing-associated-files">Potential definition and directory containing associated files</a></li>
<li><a class="reference internal" href="#initial-system-configuration-to-load">Initial system configuration to load</a></li>
<li><a class="reference internal" href="#stacking-fault-defect-parameters">Stacking Fault Defect Parameters</a></li>
<li><a class="reference internal" href="#units-for-input-output-values">Units for input/output values</a></li>
<li><a class="reference internal" href="#lammps-minimization-parameters">LAMMPS minimization parameters</a></li>
<li><a class="reference internal" href="#run-parameters">Run parameters</a></li>
</ul>
</li>
</ul>

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